super cool technique mike! I also wanted to mention that some synths have this kind of functionality built in. They allow you to use micro tuning file with the synth. which allows you to do exactly what you are doing like detuning certain notes... Synths i know support this, uhe diva, Linplug Alpha3 and Madrona Labs Aalto. I wonder if the m3 can support microtuning as well?
Another method is to make each voice can have an individual tune and you can change how it cycles through the different voices. So a single key could possibly be played at slightly different pitches depending on what order the key is playing. Uhe Diva has a really nice interface for this and The arturia CS-80v plugin also has this same type of thing(hidden in one of those fan panels) where you can control the pitch per voice.
I find this to be part of the charm with working with different hardware synths, I find them never to be tuned exactly. And I can never get anything perfectly tuned, where as in the computer it seems to be very consistent unless you go out of your way to detune. The Roland Jup6 is very good at doing this and i can't explain how... its like its in tune but not in tune. it makes the magic
I tend to record everything as audio and then put the audio into samplers and then play the keys to make sure everything is in tune. My prophet, pulse and esq1 seem to have different tunes so its the only way i can get around it. either that or i tune the oscs on each synth one to make them fit in, but i prefer to play off the keyboard so i tend to do it that way.
i always thought c1 was going to be the same on each bit of equipment, as i come from vsti's and they all fall in tune with no problems.